There has been known a fuel cell system that includes: a gas-liquid separator storing and separating water from a fuel gas discharged from a fuel cell; and a discharge valve connected to the gas-liquid separator and discharging the fuel gas to the outside together with the stored water in the gas-liquid separator. When such a discharge valve is opened, the stored water is discharged at first, and then the fuel gas is discharged. For example, Japanese Patent Application Publication No. 2007-305563 discloses technology for estimating a discharge amount of the fuel gas based on a flow rate calculated using a decrease amount of the pressure on the downstream side of an injector during a period just before and after the discharge of the fuel gas, and based on a flow rate calculated using a change amount of hydrogen consumed amount in the fuel cell.